User: Rory Stark

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Rory Stark2.6k
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CRUK, Cambridge, UK
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r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 459 results • page 1 of 46 • next >
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Comment: C: sorted the results of function dba.report in DiffBind R package
... You still need to specify a contrast number (the contrast the report was generated from). In your original call to dba.report() you used the default contrast=1, so you should add contrast=1 to the call to dba.plotHeatmap(). When no contrast is specified, dba.plotHeatmap() always uses the global bin ...
written 4 days ago by Rory Stark2.6k
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Answer: A: sorted the results of function dba.report in DiffBind R package
... The returned report should already be sorted by p-value (lowest to highest). You can change how the report is sorted based on any of the metadata columns. For example, to sort by absolute value of the fold change (greatest absolute fold change to lowest): > bptH3K27AcPeak.DB[order(abs(bptH3K27 ...
written 4 days ago by Rory Stark2.6k
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Answer: A: dba.count Can't count: some peaksets are not associated with a .bam file.
... This error arises when there is no bam file specified for a peakset. Check your sample sheet to ensure that there is a column named bamReads (case sensitive). you can check how your samplesheet looks after processing as follows: > DBA$samples You can also check all the bam file paths as follow ...
written 4 weeks ago by Rory Stark2.6k
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Answer: A: DiffBind: Error in heights * sapply(called, function(x) x)
... I've been unable to reproduce this issue. Perhaps someone experiencing it can help by sending me an example where it occurs? One thing to try would be to run the dba.count() call with summits=TRUE (instead of summits=150), then send me the resulting DBA object so I can have a look. I may be able to ...
written 5 weeks ago by Rory Stark2.6k
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Answer: A: dba.count binding matrix coordinates
... The issue is how you are retrieving the binding matrix. Accessing it directly (db$binding) results in an internal dataframe being returned. The CHR column in this is an index into a separate set of chromosome names (db$chrmap), not a chromosomes "number" . So the index of the chromosome labelled "ch ...
written 5 weeks ago by Rory Stark2.6k
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Answer: A: Use DiffBind to find differential peaks among multiple cell types
... You can add a contrast for each cell type vs. everything else, so you'd have up to 7 contrasts. You can add each contrast as follows: myDBA <- dba,contrast(myDBA, group1=!myDBA$masks$CellType1, group2=myDBA$masks$CellType1, name1="Other Cell Types", name2="Cell Type ...
written 6 weeks ago by Rory Stark2.6k
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Answer: A: How to color different column bars independently using dba.plotHeatmap (DiffBind
... You're pretty close! As per the documentation, the colSideCols value can be a list of color vectors, one for each column bar. So you can change your value to: colSideCols = list(c("orange","orchid1","mediumpurple1"), c("magenta", "cyan")) You can also pass in more parameters to the underlying plo ...
written 6 weeks ago by Rory Stark2.6k
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Answer: A: adding a new consensus peakset question
... I'd need to see how you constructed your DBA object (my.dba). Did you use dba,peakset() with consensus=TRUE? Basically if you added a consensus peakset yourself, and didn't have DiffBind computed one from a set of underlying peak sets, there is no way to know which consensus peaks are associated wit ...
written 6 weeks ago by Rory Stark2.6k
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Answer: A: diffbind finding not differential site
... The null hypothesis in these tests is that the site did not change binding affinity. Low p-value/FDR value indicate confidence that this is no true -- that there is a change. Higher p-value/FDR values,on the other hand, do not indicate confidence that the sites did not change, only that there is not ...
written 6 weeks ago by Rory Stark2.6k
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Answer: A: Differential analysis of multiple samples with different time points
... If you want to track the differences across time between two groups in a single comparison, DiffBind is not really set up to do that. You'd need to use one of the underlying analysis methods, like DESeq2, directly. There are a number of threads discussing how to set up time series analyses in DESeq2 ...
written 8 weeks ago by Rory Stark2.6k

Latest awards to Rory Stark

Popular Question 6 weeks ago, created a question with more than 1,000 views. For diffbind
Scholar 6 weeks ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 10 weeks ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 10 weeks ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 3 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 6 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 18 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 18 months ago, created a question with more than 1,000 views. For diffbind
Popular Question 18 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 18 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 18 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 18 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 18 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Popular Question 18 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 18 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind

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